Hi Carsten, > Is there an (un)documented way of merging multiple molecular objects in > Pymol into one molecule, which then can be written in a nicely formatted PDB > file? I cobbled something cludgy together with ‘multisave’ and a couple > read-sort-save cycles, but this is ugly and probably quite fragile. An API > function might be much more robust. Is there a provision like this in > ChemPy? I’ve already taken care of adjusting each molecule to be unique with > respect to chain IDs and IDs, so that would not be an issue.
It's documented: * help create * http://www.pymolwiki.org/index.php/Create Create can be used to create a single single-state object or a single multi-state object. The former will just 'do what you say' but may create biologically unrealistic molecules (it just combines the objects). The latter is better as it saves to biologically realistic multi-state pdbs. Try these examples: # method 1 # create a single state (possibly biologically infeasible) molecule # from two objects frag ala frag cys save test.pdb, ala or cys Now load "test.pdb". # method 2 # create a single multi-state object from two molecules frag ala frag cys create test, ala, 1, 1 create test, cys, 1, 2 save test.pdb, test, state=0 Cheers, -- Jason On Thu, Jun 16, 2011 at 3:58 PM, Schubert, Carsten [PRDUS] <cschu...@its.jnj.com> wrote: > Hi, > > Is there an (un)documented way of merging multiple molecular objects in > Pymol into one molecule, which then can be written in a nicely formatted PDB > file? I cobbled something cludgy together with ‘multisave’ and a couple > read-sort-save cycles, but this is ugly and probably quite fragile. An API > function might be much more robust. Is there a provision like this in > ChemPy? I’ve already taken care of adjusting each molecule to be unique with > respect to chain IDs and IDs, so that would not be an issue. > > Any pointers would be appreciated. > > Cheers, > > Carsten > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
